High-Resolution Fine Mapping and Fluorescence in Situ Hybridization Analysis of Sun, a Locus Controlling Tomato Fruit Shape, Reveals a Region of the Tomato Genome Prone to DNA Rearrangements

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ABSTRACT

The locus sun on the short arm of tomato chromosome 7 controls morphology of the fruit. Alleles from wild relatives impart a round shape, while alleles from certain cultivated varieties impart an oval shape typical of roma-type tomatoes. We fine mapped the locus in two populations and investigated the genome organization of the region spanning and flanking sun. The first high-resolution genetic map of the sun locus was constructed using a nearly isogenic F^sub 2^ population derived from a cross between Lycopersicon pennellii introgression line IL7-4 and L. esculentum cv Sun1642. The mapping combined with results from pachytene FISH experiments demonstrated that the top of chromosome 7 is inverted in L. pennellii accession LA716. sun was located close to the chromosomal breakpoint and within the inversion, thereby precluding map-based cloning of the gene using this population. The fruit-shape locus was subsequently fine mapped in a population derived from a cross between L. esculentum Sun1642 and L. pimpinellifolium LA1589. Chromosome walking using clones identified from several large genomic insert libraries resulted in two noncontiguous contigs flanking sun. Fiber-FISH analysis showed that distance between the two contigs measured 68 kb in L. esculentum Sun1642 and 38 kb in L. pimpinellifolium LA1589, respectively. The sun locus mapped between the two contigs, suggesting that allelic variation at this locus may be due to an insertion/deletion event. The results demonstrate that sun is located in a highly dynamic region of the tomato genome.

FRUIT development commences with the development of carpel or gynoecium primordia within the floral meristem. The ovary, located at the base of the gynoecium, houses the ovules, which, after fertilization, promote the ovary to develop into a fruit. In recent years, molecular genetic approaches to dissect complex pathways of floral and fruit development have largely focused on a few model species. This research has resulted in a considerable increase in knowledge of plant development and the realization that genes and pathways regulating development have been largely conserved within the plant kingdom. However, relatively little focus has been placed on molecular processes underlying biological diversity. A greater understanding of the molecular nature underlying variation and diversity can provide additional insights into the regulation of biological processes.

Years of domestication and selection for its fruit characters have resulted in a substantial diversification of tomato fruit form. Quantitative genetic analyses have led to the identification of loci that control tomato fruit morphology (GRANDILLO et al. 1999). The subsequent cloning of genes underlying fruit morphology traits is of high importance, as those genes would reveal the molecular basis of tomato domestication, while also revealing the developmental pathways affected by alleles of these loci. Typically in tomato, successful map-based cloning experiments have relied on a set of introgression lines, each containing a segment of a distant wild relative of tomato, L. pennellii accession LA716, in an otherwise Lycopersicon esculentum background (ESHED and ZAMIR 1994). The level of nucleotide polymorphisms is sufficiently high between L. esculentum and L. pennellii, thus greatly expediting molecular marker development and hence map-based cloning of the gene of interest. These tomato introgression lines have been used extensively to clone genes underlying quantitative (FRARY et al. 2000; FRIDMAN et al. 2000) as well as qualitative (PNUELI et al. 1998; ISAACSON et al. 2002) traits.

Chromosomal rearrangements occur during evolution and may involve major structural changes such as inversions and translocations as has been outlined in the grasses (WILSON et al. 1999). Between tomato and potato (Solanum tuberosum), there are thought to be five major inversions involving chromosomes 5, 9, 10, 11, and 12 (TANKSLEY et al. …